Why are bpy.ops.transform.rotate() and resize() missing black arrow visual indicators?
The visual indicator that follows the mouse doesn't appear because when you use a button in the Tool Shelf to invoke an operator, the mouse is in a region separate from the actual 3D View, which is where the operator takes place. Here are the region types, taken from https://docs.blender.org/api/blender_python_api_2_78_4/bpy.types.Region.html:

[‘WINDOW’, ‘HEADER’, ‘CHANNELS’, ‘TEMPORARY’, ‘UI’, ‘TOOLS’, ‘TOOL_PROPS’, ‘PREVIEW’]


Rotate and Resize are operators that will not draw their visual indicators if they are not invoked in the proper region. If you call these same operators from the search menu (Spacebar) and the mouse is in the 3D View's region instead of the Tool Shelf's region, the indicators will appear.

Additionally, if you press R to rotate an object with the mouse inside the Tool Shelf (Region Overlap must be enabled in the User Preferences for this to work, unless you use the search menu instead of R), the indicators will still not appear, for the same reason that it doesn't work with buttons.